There are many things to consider when thinking about how climate change might affect the food chain. I might consider how climate change may affect upwelling (bringing nutrient rich water to the surface...how will nearshore waters experience water column mixing) and if an increase in temperature reduces zooplankton species richness/composition and biomass in areas where upwelling occurs. Will there be an increase in UV radiation in surface waters? Will there be an increase in harmful algal blooms in those coastal areas receiving nutrients? It really depends on what your research interests are and why you have chosen zooplankton and climate change to study. Do you want to know if these combinations will alter food web dynamics or fisheries in the future? What questions are you interested in answering?
Actually the climate change related to El Niño, affects the upwelling a lot, and I believe that here on the coast of Brazil there is still no study that focuses only on upwelling, zooplankton, and El Niño. I am trying to think of something like changes in abundance, composition, and loss of functional groups, but I don't know where to start yet.
Have you thought about finding information on historic zooplankton composition and creating a long-term dataset that you could apply climate changes to see if there were any temperature influences on species composition? Then maybe looking at any trends in nutrients over time that might have occurred at the same time, so that you could apply trends from El Niño or La Niña from detailed literature reviews. You may be able to develop some experiments and/or sample collections to add to those datasets. When collecting current samples, you can find what species are missing or if new/different species are occurring.