Globally, estuaries are recognised as highly dynamic environments which support diverse and productive flora and fauna, and provide numerous goods and services for human wellbeing.These systems are under threat from growing coastal populations that demand the transformation of natural land to accommodate urbanisation, agriculture, harbour, and infrastructure developments. Direct and indirect land-use/land-cover (LULC) changes adversely affect estuarine water quality, directly impacting estuarine biota such as fishes.While the short links between these components are known, few studies have attempted to integrate these links, particularly within the South African context. Therefore, this study aimed to integrate different levels of assessment (LULC and estuarine water quality) to describe changes in estuarine fish ecology over space and time. The study compared two permanently open estuaries in KwaZulu-Natal with distinct land-cover types, namely the uMgeni and uMlalazi estuaries. The uMgeni Estuary is surrounded by urban features and is situated in a highly developed catchment, whereas the uMlalazi is near-natural, with some surrounding agricultural areas.Historical land-cover imagery from the estuary to the 20 m topographical contour (inclusive of the Estuary Functional Zone), the estuary catchment land-cover, water quality and ichthyofauna data were collected. Land-cover types were grouped into eight categories and 42 feature classes based on modifications to the South African National Land Cover system, the United States Geological Survey and the Coastal Change Analysis Program. Multivariate statistical analysis identified two distinct groupings of land-cover types, Period 1 (before 1989) and Period 2 (during and after 1989). This period factor was then further used throughout the study to determine associated (temporal) responses in water quality and fish assemblages. Strong negative correlations were observed between dissolved oxygen and artificial land-cover types in the uMgeni Estuary. The results suggested that the uMgeni Estuary receives nutrient inputs from various urban activities, which reduce oxygen levels within the water column. Alterations to the hierarchical ichthyofauna structure in the uMgeni occurred on a year to year basis, relative to these anthropogenic impacts. In contrast, good water quality likely associated with fewer developments within the Estuarine Functional Zone has allowed the hierarchical fish structure in the uMlalazi Estuary to remain the same over time, although minor species level differences have occurred.