Dataset associated with the paper "Integrating multiple species connectivity and habitat quality into conservation planning for coral reefs”. The data was collected using biophysical modelling (for connectivity) and remote sensing techniques (for stressors). For connectivity, data on coral reef locations and extents were obtained from the Brazilian Ministry of the Environment database. Data on daily ocean current velocity from 2008 to 2012 was obtained from the Atlantic Operational Real Time Ocean Forecasting System (Atlantic RTOFS) and used to represent ocean dynamics in the dispersal model. Data on stressors were: fishing intensity (Google Earth Pro and government reports); thermal stress (NOAA AVHRR); sedimentation (MODIS Aqua); coastal development (DMSP/NOAA/NGDC). Brazilian reefs were used in the study. Data was collected to demonstrate how functional demographic connectivity for four candidate reef-associated species with varying dispersal abilities and a suite of connectivity metrics weighted by habitat quality can be used to set conservation objectives and inform marine protected area placement.