A small standing-water ecosystem (SWE) is a shallow (<20 m) lentic water body with a surface of a few hectares (≤10 ha). Compared to larger counterparts, they exhibit wider ecotones, sometimes even equaling their whole surface, which maximizes structural heterogeneity, supporting exceptionally high biodiversity, metabolic rates, and functionality. Surprisingly, no binding regulations support global strategies for SWE conservation. This work consists of a literature review performed for the period 2004–2018 to assess the ecological and conservation value of SWEs and the contribution of the Water Framework Directive (WFD) in promoting their conservation. Outcomes from this work open new perspectives on SWEs, which emerge as valuable ecosystems, and confirm their pivotal contribution to watershed biodiversity, resilience, and functionality. Results also suggest clear narrative trends and large knowledge gaps across geographical areas, biological components, and target issues. Additionally, we note that SWEs are under-represented in the frame of WFD implementation, stressing their marginality into assessing procedures. All of this calls for further studies, especially outside Europe and with a global, multi-taxon perspective. These should be devoted to quantitatively assess the roles of SWEs in maintaining global water ecosystem quality, biodiversity, and services, and to prioritize management actions for their conservation.