Flats fisheries support valuable socioeconomic activities and are increasing in popularity as a key component of conservation practices. Despite their high value, population assessments and ecological studies are limited, and key information on life history dynamics are lacking. In the past decades, recreational catches of bonefish (Albula vulpes) have decreased significantly throughout South Florida (SFL). The mechanisms driving these declines are unknown, yet concerning given the socio-economic value of the fishery. Here we asked: 1) What are the spatiotemporal patterns of bonefish throughout SFL? and 2) What factors could be driving this decline? We used a combination of fisheries-dependent data (FDD) and local ecological knowledge (LEK) to assess the nature of the temporal trend (i.e., gradual vs. punctuated decline) in bonefish abundance in SFL. We also used different statistical modeling approaches to examine the relative importance of water quality, climatic parameters and habitat dynamics in driving bonefish numbers. Both FDD and LEK assessments pointed to the decline in bonefishing in SFL since the early 1980s, as well as, an accelerated decline that started since the late 90s-early 2000s that resulted in an overall 42% and 60% reduction in catch and perceived bonefishing quality. The results also show that the core of bonefishing significantly shifted southward over time. Over the 35 years of data, the bonefish timeline tracks the changing climate and hydrology of Florida Bay. Also, we captured evidence of causation for high temperatures and fishing pressure. These results point to the need for bonefish conservation efforts to encompass both juveniles and adults, to tackle both local and regional factors, and to consider the stronger connection between healthy bonefish fisheries and coastal water management.