Sustainable aquaculture requires the efficient use of natural pond resources as well as supplements to meet the dietary requirements of fish species. However, aquaculture diets are often produced without considering the lysine content of the natural production in the pond. As such, two plant-based diets, a control diet (L-Con) supplemented with 5.00 g lysine kg−1 diet and a lysine deficient diet (L-Def) without supplementation were fed to Nile tilapia raised in ponds with five replicates ponds for each diet. The aim was to investigate the effect of L-Def diet on plankton selectivity, metabolic growth, haemato-biochemical parameters, gut content and intestinal morphometry. Fish were fed a fixed ration of 18 g kg−0.8 d−1 for 10 weeks. During the experimental period, plankton species in the fish guts were identified and categorised to phylum level: phytoplankton phyla – Euglenophyta, Bacillariophyta, Cyanobacteria, and Chlorophyta; zooplankton phyla - Copepoda, Rotifera, and Cladocera. Fish in ponds receiving the L-Def diet selected positively for all phyto and zooplankton phyla but the selectivity was only significantly higher for Bacillariophyta with fish in ponds receiving the L-Con diet (P