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India has a large spread of freshwater resources in the form of rivers, reservoirs, lakes and ponds. For aquatic fauna, the nature of substrate assumes substantial importance in terms of quantity and quality of their productivity. Substrate includes both solid, liquid and gas which have complimentary effects. For brevity, this paper discusses the effect of solids with special reference to soil substrate and its effect on meat quality. Matter suspended in water may be organic and inorganic, as is common in soils. Inorganic matter constitutes ~ 99% and the rest is organic in most of the tropical soils. In aquaculture, organic matter should be 1.5-2.5% with an average C: N ratio of 10- 20 since it indicates moderately fast mineralization. Although the crucial importance of sediments in aquatic systems is well known, sediments are not considered as a factor in the evaluation of water quality assessment. Few studies with zebra fish Danio rerio (a freshwater fish) showed that river samples comprising both water and sediment exert pivotal effects in embryos, whereas surface water alone did not. This is in contrast to the findings of German rivers (Neckar, Rhine and Danube) showing high to very high embryotoxic potentials in sediments. Nevertheless this serves as a reminder that sediments have to be taken into account for the biological assessment of ecosystem quality. Urbanization and increased agricultural activities caused long term changes to many of the key physical characteristics in coastal environment. Many shallow water coastal habitats have already been severely modified through changed sedimentation regimes, increased nutrient loading, elevated turbidity and reduced light penetration. The effects of fine sediments on fish have been especially well documented. Increased turbidity and reduction of instream habitat heterogeneity are often cited as critical factors affecting fish community diversity, community structure and productivity. Influence of coarse sediment on fish productivity has not yet received much attention. In some aquaculture experiments, catla, rohu, silver carp and common carp were raised with organic manures for organoleptic evaluation. Odour of flesh and texture of meat of rohu were found better suggesting no adverse effect on the acceptable qualities of the carps by treated sewage. However, the growth, morphometry and keeping quality of fish from river channels with eutrophication indicated body deformities, reduced growth rate, and flesh quality deterioration. Indepth studies are necessary to assess the biological and structural fish quality from stresses using environmental descriptors, isotope studies and molecular markers