Globally, declines in freshwater biodiversity have been recognized to be far greater than those in marine or terrestrial realms. And like the rest of tropical Asia, the Philippine freshwater ecosystems and their biodiversity have been neglected. Our goals in this review are to provide indications where further research is needed, what systems are underrepresented and which organisms have been neglected. In this study, we determined the current knowledge on freshwater ecosystems in the country through critical evaluation of available peer-reviewed literature. A structured search on studies on Philippine freshwater systems published from January 1988 to December 2012 was performed using the Thomson Reuter’s Web of Science and Zoological Records. A total of 281 papers that have directly assessed Philippine freshwater systems and/or have actually collected and examined aquatic organisms from these systems were included in the review. More than 70% of the papers were produced solely by local researchers or with international collaborators. There was a significant steady increase in Philippine freshwater studies, with systematics (105 papers) and freshwater fish (78 papers) being the most frequently studied research area and organism, respectively. Rivers (116 studies) and lakes (112 studies) are still the most frequently studied freshwater systems. Among the papers reviewed, Luzon freshwater systems were the focus of most studies with Laguna de Bay being the most researched. Freshwater systems in the Visayas and Mindanao received little research attention. Finally, we presented a four-point research agenda, the results of which could form the basis for policy or management decisions to aid future conservation and sustainable management of freshwater ecosystems and their biodiversity in the Philippines.
