"The fish dying here at Nyandiwa is bad for us because now the prices are down and even when you're fishing and you have a catch, nobody will buy from you, as the women folk selling fish say you have brought the spoilt dead fish," said Godfrey Otieno , a Kenyan fisherman.
Experts say the deaths are caused by low oxygen levels in the lake.
"And when these fish die, the process of decaying begins, and when they decay that process also uses oxygen, so they further deprive water of oxygen making the water environment completely inhabitable for fish especially the Nile perch that has a high oxygen requirement", said Chris Nyamwea, the assistant director of Kenya's Maritime and Fisheries Institute.
Authorities in both countries have ruled out poisoning.
Uganda's ministry of agriculture said in January that the deaths were a 'usual phenomen' caused by hypoxia, a condition which causes water to mix, thereby reducing the oxygen levels in the lake.
Industries, farms and settlements near Lake Victoria have also been blamed for polluting its waters.
Fish is one of the east African countries' top exports.
Millions of people in Uganda, Tanzania and Kenya depend on Lake Victoria for their livelihood.