TANJUNG LEIDONG, Indonesia — At around 5:30 a.m., after the tide starts to recede, Zulkifli Dalimunthe rushes to the shore a stone’s throw from his house, where he anchors his small wooden boat.

Small-scale fishers in Indonesia face declining catches as illegal trawlers deplete fish stocks in near-shore waters, violating exclusion zone regulations. Trawling, a destructive fishing method ...