Limnological tools to improve water transparency management in semi-intensive cultures of Oreochromis niloticus

The aim of this study was to evaluate the relationships among water quality variables and Secchi disk transparency in semi-intensive Oreochromis niloticus earthen ponds. A total of 38 water samples were taken from 27 O. niloticus culture ponds located in rural villages in Brazil, using a non-probabilistic convenience sampling approach. The main water quality variables analyzed included transparency, chlorophyll- a, total suspended solids (TSS), inorganic solids (IS), and volatile solids (VS). The results demonstrated that Chl a (p -value = 0.04), TSS (p -value = 0.002), IS (p -value = 0.02), and VS (p -value = 0.04) had a significantly increasing trend with decreasing pond Secchi disk transparency. These findings indicated that the low water transparency readings were not caused solely by system’s primary production This was confirmed by the high percentage of IS in the TSS (> 60%), reinforcing the idea that solids in the water were composed of mineral particles such as sand, silt, and clay. This behavior could be caused by wind or bioturbation by O. niloticus, which causes sediment from the bottom of the pond to be carried into the water column, reducing water transparency. These findings demonstrated that water transparency was not directly related to pond primary production. Therefore, relying solely on Secchi disk depth, as commonly practiced, may not be sufficient for managing eutrophication in semi-intensive O. niloticus farming through water exchange. These results highlight the importance of accurately interpreting water transparency to support more effective environmental management, reduce potential stressors, and contribute to improved animal welfare in these farming systems.

Aquaculture fish production has surpassed capture fisheries production (FAO, 2024), representing a powerful resource for ensuring food security worldwide. Among the top species produced by aquaculture, tilapia (Oreochromis niloticus) ranks fourth, followed by shrimp (Penaeus vannamei), oysters of the genus Crassostrea, and the grass carp (Ctenopharyngodon idellus) (FAO, 2024). According to Food and Agricultural organizations report, the total production of O. niloticus in 2022 reached 5.3 million tons (FAO, 2024). O. niloticus is broad-based omnivorous fish that feeds on detritus and benthic fauna (FAO, 2009). Due to their high tolerance to environmental stressors, this species is resistant to wide variations in water quality conditions and stocking densities (FAO, 2009). These key characteristics enable it to be cultured in different farming systems, presenting strong price competition with wild fish (FAO, 2024).

The Brazilian production of O. niloticus varies from intensive systems, adopted by large companies to semi-intensive earthen ponds widely adopted by smallholders, i.e. small companies or family production (Pedroza Filho et al., 2020). The latter relies on natural productivity stimulated through fertilization and supplemental feeding (El-Sayed, 2020). Fertilization enhances photosynthesis and promotes the growth of phytoplankton and heterotrophic microbial communities, which serve as natural food for fish (El-Sayed, 2020). However, excessive primary production may occur due to overfertilization, feed residues, and fish excretion, leading to deterioration of water quality (Boyd and Tucker, 1998). High photosynthetic activity in open ponds also causes marked daily fluctuations in key water parameters such as pH and dissolved oxygen, resulting in oxygen supersaturation during the day and depletion at night due to respiration (Pereira et al., 2022). As a result, dissolved oxygen levels may drop to critical concentrations in the early morning (Mischke, 2012). Continuous monitoring of these parameters is therefore essential for the proper management of semi-intensive cultures. In addition, maintaining stable water quality is directly associated with the reduction of physiological stress in fish, which is a key component of animal welfare in aquaculture systems (Emam et al., 2025).

Monitoring of the system’s primary production and suspended particles in the culture medium can be measured indirectly through water transparency, using cost effective devices such as Secchi disks, especially by small farmers (Boyd, 2020). Water transparency is an integrated measure of numerous chemical and biological variables in the water column that may be related to eutrophication level; suspended particles, for instance, may be either organic such as phytoplankton cells or inorganic such as suspended sediments (Esteves, 2011). In aquaculture tanks, reduced Secchi disk depth measurements are often assumed as an increase in phytoplankton abundance (i.e. an increase in primary productivity) (Boyd, 2020). In agreement to common aquacultural practices, the Secchi disk transparencies between 46 and 60 cm indicate low phytoplankton production, suggesting that fertilization should be applied to stimulate microbial growth (Mischke, 2012). Secchi disk transparencies ranging between 31 and 45 cm indicate a good level of productivity, with no fertilization required (Mischke, 2012).

Pedrazzani et al. (2020), evaluated the welfare of O. niloticus farmed in semi-intensive systems, and reported that tank Secchi depth transparencies between 22 and 31 cm indicated low dissolved oxygen concentration in the water, which was likely due to high biomass (primary producers and heterotrophs) and consequent high respiration rates. Such conditions can impose chronic or acute stress on fish, impairing physiological performance, health status, and overall welfare. Thus, under these conditions, water renewal is recommended to improve water and fish welfare quality. Moreover, the water transparency can also be affected by fish stocking density (Lertwanakarn et al., 2023), due to increased water turbidity by resuspending particulate matter from the bottom sediments. This is the case for O. niloticus, that may feed on bottom detritus and forage in the sediment (El-Sayed, 2020), resuspending sediments into the water column, increasing turbidity and, consequently, reducing water transparency. Mischke (2012) indicates that transparency levels below 20 cm originated from suspended soil particles, will result in low primary production. Therefore, in O. niloticus culture systems in earthen ponds, water transparency readings using the Secchi disk depth can be biased by the amount and type of suspended solids in the water. In practice, this can lead producers to make poor decisions regarding fertilization and water exchange management (i.e. promoting water renewal when water transparency is low due to inorganic solids in suspension instead of high phytoplankton biomass).

It is important to highlight the scarcity of studies that have investigated and understood the relationships among water quality variables and water transparency. This easy-to-use, low-cost tool is broadly employed for monitoring water quality in O. niloticus ponds. Despite its importance, the interactions among key environmental factors influencing water quality in O. niloticus culture systems remain insufficiently understood, particularly in semi-intensive earthen ponds. Addressing this gap may improve water quality management, mitigate environmental stressors, and promote better welfare conditions in these farming systems. Therefore, this study aimed at evaluating relationships among water quality variables and Secchi disk transparency in semi-intensive O. niloticus earthen ponds, with implications for improving environmental management and fish welfare.

Sampling

This study was performed in twenty-seven O. niloticus production earthen ponds on farms located in rural villages in the state of Rio Grande do Norte, northeastern region of Brazil, in a total of thirty-eight sampling events. Sampling followed a non-probabilistic convenience approach based on access granted by local farmers and pond accessibility at the time of collection. Twelve ponds were sampled in fish farms in Aracati village (Figure 1a), six in Bebida Velha 1 (Figure 1b), six in Bebida Velha 2 (Figure 1c), one each in Modelo 1 (Figure 1d), Modelo 2 (Figure 1e), and Canudos (Figure 1f).

Characterization and management of the O. niloticus ponds

All the sampled ponds employed a semi-intensive culture of O. niloticus. The ponds measured 23 m × 75 m (1725 m²), were supplied with groundwater, and had a depth of 66.8 ± 23.59 cm (mean ± standard deviation). Fertilization management of the ponds was carried out weekly by measuring water transparency using a Secchi disk. When transparency was > 60 cm, the ponds were fertilized with poultry manure to stimulate primary production. When transparency was < 30 cm, farmers promoted partial water exchange to avoid anoxic conditions (Mischke, 2012).

Sexually reverted O. niloticus fry, weighing approximately 0.5 g, were purchased from a commercial hatchery. The animals were stocked at a density of approximately 1.0 fish m -3. The grow-out period in these tanks lasted approximately six months, when the animals were harvested at an average weight of approximately 650 g. During the rearing period, the animals were fed from six to three times a day depending on the development stage of the fish. During the first 5 weeks of rearing, the animals were fed a commercial diet with 50% crude protein (Supra Pre-Juvenil. Size: 0.1 and 0.8 mm). For the following 5 weeks, the crude protein was adjusted to 42% (Supra Juvenil. Size: 2.5 mm) and lastly decreased to 32% crude protein for 8 weeks (Supra Tilapia. Size: 5 mm). The end phase of the grow-out was done for a period of 7 weeks with a diet with 28% crude protein (Acqua Fish. Size: 8 mm), following established nutritional requirements for O. niloticus (El-Sayed, 2020).

Fish farms were structured into modules of six ponds (or multiples of six, depending on farm size), with one pond per module being stocked each month. This sequential stocking scheme results in a six-month production cycle, such that once all ponds are stocked, the first pond reaches the harvest phase. Consequently, at any given time, ponds within a module are at different stages of cultivation, which should be considered when interpreting temporal patterns in water quality and production metrics. This approach was adopted to account for the staggered production system used in the farms, where ponds within each module were sequentially stocked and harvested, leading to asynchronous cultivation stages. As a result, the sampling design captured both temporal variation within ponds and variability across different production stages. All the samplings were considered as independent observations.

Water sampling and water quality variables

Samplings were performed on May 25 th, August 27 th, September the 3 rd, and October 13 th, 2010. Water was sampled from the subsurface at a single point near the pond drain and stored in 1.5 L polyethylene bottles. The samples were stored in the dark at low temperature (ca. 4°C) and taken for analysis to the Laboratório de Limnologia of the Universidade Federal do Rio Grande do Norte (UFRN) within a period of less than 3 hours.

In all ponds, water transparency was estimated through Secchi disk depth, dissolved oxygen (DO, mg L -1), pH, and temperature (°C) with a multiparameter probe (Horiba, model U-22). In the laboratory, bulk water samples were used to determine total phosphorus (TP, µg L -1) and total nitrogen concentrations (TN, µg L -1) concentrations. Each water sample was homogenized and divided into subsamples. One subsample was filtered through a 1.2 µm filter (GF-3, Machenery Nagel) for the determination of total dissolved phosphorus (DP, µg L -1) and total dissolved nitrogen (DN, µg L -1). The filters were used to determine the concentrations of Chlorophyll- a (Chl- a, µg L -1), total suspended solids (TSS, mg L -1), inorganic solids (IS, mg L -1), and volatile solids (VS, mg L -1). The percentage of IS and VS in the TSS was also calculated. TN and DN were determined from unfiltered and filtererd water, respectively, and persulfate oxidation was used to convert all nitrogen forms to nitrate. Both nitrogenous forms were analyzed by photometric methods following Valderrama (1981) and APHA (1998). For the TN and DN analysis, standard curves were prepared with potassium nitrate (KNO 3) and ultrapure water. For TP and DP analysis, standard curves were prepared with potassium phosphate (KH 2 PO 4) and ultrapure water. Sample readings were performed in triplicates, and blanks were prepared with ultrapure water, with resolution of one decimal case. Particulate phosphorus (PP, µg L -1) and particulate nitrogen (PN, µg L -1) were determined by subtracting the concentration of total fractions from the dissolved fractions. Furthermore, the total particulate, and dissolved nitrogen:phosphorus (N:P) ratios were calculated from the molar concentration of each phosphorus and nitrogen fraction (as in They et al., 2017).

The pigments for Chl a estimation were extracted with ethanol 90% for 18 h at -20 °C and then estimated by spectrophotometry (Varian Cary 100 Conc UV–Vis) at 665 and 750 nm (Jespersen and Christoffesen, 1987). Sample readings were performed in triplicates, and blanks were prepared with ethanol. TSS and IS were determined by gravimetry (scale resolution of 0.00001 g) after drying filters overnight at 100 °C and igniting them at 500 °C for three hours, respectively (APHA, 1998). The VS were measured by the difference between total suspended solids and inorganic suspended solids (APHA, 1998). IS were used as a proxy of inorganic turbidity and the volatile solids (VS) as a proxy of organic turbidity.

Data analysis

A descriptive analysis was performed for the water quality variables measured in the O. niloticus ponds and presented as mean, standard deviation, median, maximum, and minimum. Simple linear regressions were built to test the relationships among the water quality variables. The assumptions of normality and homoscedasticity were tested with the Shapiro-Wilk test and Global Validation of Linear Model Assumptions (GVLMA) function, respectively. The data were log-, square-root-, or cosine-transformed to fulfill parametric assumptions. An α = 0.05 was adopted as the criterion of statistical significance.

The map, graphs, and linear regressions were performed in R software, version 4.3.1 (R Core Team, 2023) with the packages gvlma (Pena and Slate, 2019), ggplot2 (Wickham, 2016), devtools (Wickham et al., 2022), ggmap (Kahle and Wickham, 2013), and mapproj (Brownrigg et al., 2022).

The main environmental variables were indicative of typical high temperatures for this latitude, well oxygenated waters and slightly alkaline pH. The mean transparency was in general around the lower limit for desirable productivity levels (31 to 45 cm, Mischke, 2012), whereas mean chlorophyll was above 100 µg L -1. On average, around 60% of total suspended solids were inorganic (non-volatile). Roughly 50% of the total nitrogen and phosphorus were in the dissolved form. The mean stoichiometric ratios indicated a surplus of N in relation to phosphorus in total, dissolved and particulate forms, compared to the classic 16:1 N:P Redfield ratio (Table 1).

There were recorded significant negative linear regressions between Chl a (R² = 0.15 and p -value = 0.04), TSS (R² = 0.60 and p -value = 0.002), IS (R² = 0.41 and p -value = 0.02), VS (R² = 0.32 and p -value = 0.04) with the Secchi depth transparency. These significant relationships are displayed in Figure 2. On the other hand, temperature, DO, pH, nutrients concentrations (TP, DP, PP, TN, DN and PN), total, particulate and dissolved N:P did not present significant relationship with Secchi depth transparency (Supplementary Table 1). Likewise, neither TSS nor Chl a present significant relationships with neither TP, DP, PP, TN, DN, PN, total, particulate or dissolved N:P (Supplementary Tables 2, 3). Finally, TSS and Chla did not present a significant relationship (Supplementary Tables 2, 3).

Drivers of turbidity in earthen ponds

Aquaculture pond management usually assumes that water transparency (e.g., Secchi disk depth) primarily reflects the concentration of suspended organic components, particularly phytoplankton (algae and/or cyanobacteria) or heterotrophic organisms such as microbial flocs and zooplankton. This assumption generally holds for lined tanks, where sediments are not in direct contact with the water column (Hargreaves, 2013; Boyd, 2020). In such systems, there is a well-established successional pattern of initial clear water with high phytoplankton concentration, that progressively collapses with increasing turbidity due to bioflocs maturation and accumulation (Silva et al., 2013). Thus, turbidity is mainly associated with organic solids, that might shift from dominance by primary producers to heterotrophic microorganisms as in biofloc systems (Silva et al., 2013).

In contrast, earthen ponds may introduce an additional source of turbidity through sediment-water interactions (Mischke, 2012). Our results support this distinction even in phytoplankton-dominated systems. Even though Chl- a increased with decreasing water transparency (Figure 2a) this relationship became highly variable at low transparency levels, i.e. Secchi depth transparency lower than 40 cm (Figure 2a). This pattern indicates that reduced transparency was not exclusively associated with primary production. Instead, our findings suggested that resuspended solids played an important role in controlling water transparency. The high proportion of inorganic solids within total suspended solids (Table 1), together with the negative relationships between transparency and TSS, IS and VS, supports this interpretation (Figures 2b–d). These particles likely originated from sediment resuspension processes, which are commonin shallow aquaculture ponds and can be driven by wind action or fish activity (Mischke, 2012; Boyd, 2020). Resuspended solids from the sediment in aquaculture ponds are usually composed of organic particles, mainly feces, residual feeds and dead phytoplankton cells; and inorganic particles such as soil derived material such as clay, silt and mineral nutrients (Avnimelech et al., 1999; Jiménez-Montealegre et al., 2002; Kassila and Hussenot, 2006; Hoess and Geist, 2022).

Boyd (1995) reported that aquaculture bottom-feeding fish stocked ponds experience sediment resuspension, which promotes intense nutrient exchange between the pond bottom and the water column. In fact, it was previously recorded that O. niloticus activity in shallow lakes causes significant sediment resuspension (bioturbation) with negative consequences to light incidence and primary production, contributing to inorganic turbidity (Zhang et al., 2017; El-Sayed, 2020). The sediment resuspension rate may be related to the weight and quantity of fish stocked. Nonetheless, it can be caused by the foraging process at the pond bottom or by the intense movement of fish during the feeding process (Jiménez-Montealegre et al., 2002). Thus, higher transparency and lower suspended solid concentrations are likely to occur during the early phases of culture. At this stage, the biomass of primary producers are still low, and O. niloticus individuals are small, exerting limited bioturbation. On the other hand, at late stages of culture, the higher biomass may trigger higher sediment resuspension rates (Zhang et al., 2017; El-Sayed, 2020), which might increase the role of inorganic solids and organic (detritus) solids to reduce water transparency.

Inorganic solids are composed of gravel, sand, silt, clay, and mineral particles suspended in the water (Zezulka et al., 2024). High levels of inorganic suspended particles may contribute to suboptimal environmental conditions, potentially affecting fish health and welfare through chronic exposure to turbidity and associated water quality fluctuations. Nonetheless, this condition likely occurs when fishes need to allocate energy to growth which may negatively affect welfare and biomass production (Makori et al., 2017; Abdel-Tawwab et al., 2019). Thus, high turbidity when present high proportion of resuspended sediments might present negative effects on fish biomass yield, rather than fish-feeding supplementation.

Implications for pond management and fish welfare

Even though O. niloticus is usually planktivorous and filter-feeding, our results provide strong evidence that this culture may also drive ponds to an inorganic turbidity state from sediments resuspension, which is usually expected in benthivores fishponds (e.g., silver and common carp; Mischke, 2012). This was evidenced by the less pronounced relationship between Chl a and transparency, while TSS was strongly related to it (Figure 2). Moreover, IS accounted for more than 60% of the TSS, likely caused by resuspension from the bottom of the tank. Therefore, the common management approaches would be inefficient to improve fish production quality. Here we demonstrate this alternative scenario recorded for the filter-feeding O. niloticus and discuss the mechanisms behind these dynamics. From a welfare perspective, this finding is particularly relevant, as misinterpretation of turbidity sources may lead to inadequate management decisions, potentially exacerbating environmental stresses instead of mitigating it.

The maintenance of the transparency at a certain level (e.g., transparency between 30 and 45 cm) is essential to fish production stability (Mischke, 2012). Thus, when transparency increases, ponds should be fertilized to promote algal growth as alternative natural feed. On the other hand, when transparency is low (e.g., as low as 30 cm or less), ponds are under very eutrophic conditions, e.g. high Chl a and nutrients (N and P), with chances to experience anoxic episodes and dominance of harmful/toxic cyanobacteria (Kubitza, 2013).Furthermore, an exacerbated increase in suspended solids and reduced water clarity may impair gill functioning and increase energetic costs for fish, representing a potential environmental stressor in pond systems (Guo et al., 2026). In this sense, the common practice recommends partial water change to reduce the risks of anoxic and toxic conditions by removing nutrients and primary producers’ biomass. On the contrary, our study proposes an alternative scenario where sediment resuspension (due to winds or fish bioturbation) plays the major role in transparency. Consequently, management actions based solely on transparency thresholds, without considering turbidity origin, may fail to prevent stressful conditions such as oxygen depletion or excessive particulate matter in suspension (Boyd and Tucker, 1998) and do not improve fish productivity (Figure 3).

Importantly, such mismanagement may also compromise fish welfare, as inappropriate fertilization or water exchange practices can intensify environmental instability and stress within the culture system. Therefore, tools that help identify the origin of turbidity should be adopted. For instance, the color of suspended solids can provide a simple diagnostic indicator, with green particles typically associated with phytoplankton and brownish particles with resuspended sediments. This approach, as demonstrated by Pimentel et al. (2023) in biofloc-based shrimp systems, may support more accurate management decisions and ultimately improve fish performance and welfare. It is important to emphasize that this study was limited by its non-probabilistic sampling design and observational nature, which may restrict the generalization of the findings and preclude definitive causal inferences. Although total and inorganic suspended solids were quantified, sediment resuspension was inferred indirectly by the shallow nature of the fishponds and by the fish behavior. As direct measurements of particle fluxes or near-bottom turbidity dynamics (e.g., sediment traps or high-frequency sensors) were not performed, the variability among ponds may not have been fully controlled.

The concentration of chlorophyll a, total suspended solids, inorganic solids, and volatile solids had a significant negative relationship with transparency in semi-intensive culture ponds of O. niloticus. However, differently from other production systems where transparency is related to organic particles (phytoplankton, zooplankton and microbial flocs), in these earthen ponds transparency was overall better explained by TSS variation, which in turn was composed mainly by inorganic (non-volatile) solids. This distinction is crucial, as the origin of turbidity directly influences management decisions and the resulting environmental conditions experienced by fish. This pattern may be associated with sediment resuspension processes linked to O. niloticus activity or wind, and indicates that low transparency may not be completely related to high primary production in the system and could be driving fish farmers to inefficient management practice to promote fish biomass production. Therefore, a more accurate interpretation of water transparency, considering the origin of suspended solids, is essential not only to optimize production but also to support improved environmental conditions and welfare in semi-intensive O. niloticus farming systems. Future research should include controlled and high-resolution approaches to better quantify sediment resuspension dynamics, assess temporal-spatial variability within ponds, and evaluate how different management practices influence the relationship between suspended solids and water transparency in semi-intensive culture ponds of O. niloticus.