This study evaluated the presence of selected heavy metals in farmed tilapia and catfish) in Nyeri County, Kenya. Live fish comprising of 17 catfish and 33 tilapias were purchased from 15 fish farmers with 31(62%) caught from earthen ponds while 19 (38%) were from liner ponds. The fish were dissected to obtain muscle tissue samples for analysis for levels of lead, mercury and cadmium residues using the Flame Atomic Absorption Spectrometry. Tilapia fish accumulated higher concentrations of lead, mercury and cadmium in the muscles compared to catfish. The difference of lead and mercury ion concentration between fish species was not significant (p>0.05). Fish obtained from earthen ponds recorded a higher mean concentration of the three heavy metals compared to those from liner ponds. Mercury concentration in fish muscles was slightly higher than European Union limits (0.1 Mg/Kg) but lower than codex alimentarius (0.5 Mg/Kg) limits. There is need to continuously monitor levels of heavy metals especially mercury in farmed fish tissues in Nyeri County and other peri-urban areas in Kenya.