During the study of effect of hydrological alteration on physico-chemical water quality parameters of a reservoir, it was discovered that the level of Ni and Cu in the reservoir was higher than permissible concentration as stipulated by WHO.
Mostly the long term geochemical accumulation with the high percentage of particulate and fine sediments that increasing the redox potential, subsequently, Cu and Ni transform into insoluble sulphide forms within the sediment layer.
These could be due to sediment accumulation as pointed out by other answers. Here is a paper that discusses heavy metal accumulation in lake environments and the underlying conceptual framework:
One other source of Cu, Ni may be the geology of the area which may be in relation to a mine of Ni and Cu. Do you disregard the pollution that may result from electroplating waste discharge into water bodies without treatment.
I suggest looking at the sources of water inputs to the reservoir, such as agricultural or urban runoff and treated/untreated wastewater. Copper is used as a pesticide on certain crops. Copper is also used as an algacide in lakes and reservoirs. Copper is present in brake linings and other consumer products that can contaminate urban runoff. Copper from household plumbing leaches into water and can contaminate wastewater.
The sources may be variable. You have to investigate several possible factors, like e.g. enriched runoff discharges, interaction with aquifer systems ricn in these metals, ineraction with the geological background, metal release from bottom sediment due to redox conditions, external triggering factors related with land use etc. All these factors may have temporal variation as well and not be constant. I attach you a published paper in which i faced similar problems with Ni enrichment in a Lake due to the the impact of lateritic fhorizons and ophiolitic formations.