HiCustomer and welcome to JA!
The most likely reason that the flamingos are dying at Lake Nakuru is that they are consuming toxic waste that was dumped there (see the first reference below). They may have migrated to sewage ponds to feed, ingesting toxic substances. In addition, flamingos migrate to other lakes (because the lake level gets lower and their food sources get depleted).
Populations have fluctuated wildly over the past 50 years. For example, according to the second reference below, there were about 915,000 birds in 1972 and 1973, but by 1974, there were only 113,000 birds. That study found that these short time flamingo population fluctuations that are correlated with algal densities (which is one of their food sources). According to the third reference below, the lowest population of flamingos was in 1969 (about 68,000 birds), and the highest was in 1995 (about 2,800,000 birds).
Here are some refs for you to look at:
I hope this helps. Let me know if you have any questions,