This thesis is a part of Wageningen University’s Interdisciplinary Research and Education Fund project entitled “Optimization of nutrient dynamics and fish for integrated agriculture- aquaculture systems” (INREF-POND). The main objective of INREF-POND is to quantify and optimize changes in nutrient dynamics in integrated agriculture-aquaculture (IAA) farming systems after the introduction of selected fish breeds. The IAA systems are characterized by low level of inputs, and traditional, indigenous breeds of fish, cattle, pigs, goats, sheep, and poultry.