Freshwater ecosystems support highly biodiverse plant and animal populations and provide crucial ecosystem services to human communities. Despite this importance, these systems are being degraded faster than terrestrial or marine environments, resulting in large global declines in freshwater biodiversity. To track such environmental change, birds are often used as indicator species. I focused on tracking changes in significant waterbird breeding colonies, rivers and internationally listed wetlands in Botswana facing a wide range of threats. I identified that riparian bird communities along the Chobe River were more biodiverse in sites with the presence of large herbivores, highlighting the direct and indirect relationships between these seemingly unconnected taxa. Using a drone, I explored the relationships between waterbird breeding and river levels and inundation. Drone imagery on the Chobe River provided comprehensive data on the reproductive success, size and composition of the Kasane waterbird breeding colony, which were linked to river levels and inundation, while citizen science collected abundance data helped identify a threshold river level to support large waterbird breeding colonies. This underlined the importance of river flows for waterbird populations and the potential for the breeding of waterbirds to inform river management. Similarly in the Okavango Delta, citizen science data highlighted positive relationships between waterbird abundance and river flows, but there were indications of long-term declines in waterbird abundances. River flows were again important for waterbird breeding, with key waterbird breeding colonies located in areas experiencing moderate to high flood frequencies. I also developed a semi-automated counting technique for investigating colony sizes with a drone, negating the need to physically enter a colony or manually count imagery, saving time in image processing and ensuring researcher safety. Finally, I investigated the potential effects of foraging at landfill on the marabou stork. Plastics formed a significant proportion of marabou regurgitant while trace metal concentrations in feathers were higher than in naturally foraging populations, indicating potential deleterious impacts. My work highlighted the value of riparian bird communities, predominantly waterbirds, as indicators of change, reflecting herbivore population structures, land use alterations and changes in freshwater flows and inundation.