Climate change and other anthropogenic factors have caused a significant decline in seagrass cover globally. Identifying the specific causes of this decline is paramount if they are to be addressed. Consequently, we identified the causes of long-term change in seagrass/submerged aquatic vegetation (SAV) percentage cover and extent in a marine protected area on Jamaica’s southern coast. Two random forest regression (RFr) models were built using 2013 hydroacoustic survey SAV percentage cover data (dependent variable), and auxiliary and 2013 Landsat 7 and 8 reflectance data as the predictors. These were used to generate 24 SAV percentage cover and benthic feature maps (SAV present, absent, and coral reef) for the period 1984–2021 (37 years) from Landsat satellite series reflectance data. These maps and rainfall data were used to determine if SAV extent/area (km2) and average percentage cover and annual rainfall changed significantly over time and to evaluate the influence of rainfall. Additionally, rainfall impact on the overall spatial patterns of SAV loss, gain, and percentage cover change was assessed. Finally, the most important spatial pattern predictors of SAV loss, gain, and percentage cover change during 23 successive 1-to-4-year periods were identified. Predictors included rainfall proxies (distance and direction from river mouth), benthic topography, depth, and hurricane exposure (a measure of hurricane disturbance). SAV area/extent was largely stable, with >70% mean percentage cover for multiple years. However, Hurricane Ivan (in 2004) caused a significant decline in SAV area/extent (by 1.62 km2, or 13%) during 2002–2006, and a second hurricane (Dean) in 2007 delayed recovery until 2015. Additionally, rainfall declined significantly by >1000 mm since 1901, and mean monthly rainfall positively influenced SAV percentage cover change and had a positive overall effect on the spatial pattern of SAV cover percentage change (across the entire bay) and gain (close to the mouth of a river). The most important spatial pattern predictors were the two rainfall proxies (areas closer to the river mouth were more likely to experience SAV loss and gain) and depth, with shallow areas generally having a higher probability of SAV loss and gain. Three hurricanes had significant but different impacts depending on their distance from the southern coastline. Specifically, a hurricane that made landfall in 1988 (Gilbert), resulted in higher SAV percentage cover loss in 1987–1988. Benthic locations with a northwestern/northern facing aspect (the predominant direction of Ivan’s leading edge wind bands) experienced higher SAV losses during 2002–2006. Additionally, exposure to Ivan explained percentage cover loss during 2006–2008 and average exposure to (the cumulative impact of) Ivan and Dean (both with tracks close to the southern coastline) explained SAV loss during 2013–2015. Therefore, despite historic lows in annual rainfall, overall, higher rainfall was beneficial, multiple hurricanes impacted the site, and despite two hurricanes in three years, SAV recovered within a decade. Hurricanes and a further reduction in rainfall may pose a serious threat to SAV persistence in the future.