Herbivory, together with seasonal variations in temperature, light and nutrient concentration regulate macroalgal populations on coral reefs. Individual management interventions can influence this balance by altering some, but not all of these potential drivers. For example, no-take marine protected areas (MPAs) on coral reefs can increase herbivorous fish abundance, thereby decreasing macroalgal coverage, but have limited influence on water quality and other vagile drivers. We compared the relative influence of seven abiotic water quality variables to that of MPA status on macroalgal coverage in 14 sites (5 of which are within no-take MPAs) over four consecutive seasons (summer through to spring) within the marginal coral reef habitats of Moreton Bay, Australia. Algal cover was quantified by taking 100 photo quadrats per site per sampling with the relative importance of our eight factors determined statistically by generalised additive models. Overall, temporal variations in total macroalgal cover and four out of five important macroalgal genera correlated with factors other than marine protection, especially water temperature, salinity, water clarity (Secchi disc) and nutrient concentration (nitrogen and phosphorus). However, seasonal variations in cover of individual macroalgal genera did not follow strong temporal trends and were not consistent with total macroalgal cover, meaning that different factors were significant for different algal genera. Consequently, we advocate for caution in determining the influence of impact gradients by exclusively measuring total macroalgal cover. This study highlights the importance of considering local impact gradients and habitat recovery processes in the design of protected area networks.