Archaeological research conducted in Morocco over the last two decades has revealed a wealth of diachronic maritime cultural heritage resources, under water and in the coastal zone. However, observation and study has revealed that natural and anthropogenic threats are impacting these resources. Given the challenges to managing maritime cultural heritage (MCH) resources in a country with such an extensive coastline and limited human managerial resources, the national heritage agency and external research institutions have developed methodologies that in part aim at mitigating these threats. This development is illustrated through three projects, briefly outlined here: the Oued Loukkos Survey, the CBDAMM Project and the MarEA Project. These projects incorporate approaches that have been tailored to the Moroccan context, considering the type of resources, the extent of the coastline, types of threats, legislation, and people and institutions involved. In conclusion, this article stresses that an interdisciplinary methodological approach to documentation is necessary in order to inform successful mitigation strategies and to plan for future interventions of MCH.