We applied two recent approaches largely used in biological conservation: Threat Analysis (TAN) and Threat Reduction Assessments (TRAs), assessing the effectiveness of a project focused on two water-related bird species (common tern, Sterna hirundo and little tern, Sternula albifrons), commonly breeding in some wetlands of Italy. We used the IUCN standardized lexicon for the classification of threats, utilizing a panel of experts to assess a set of regime attributes (extent, severity and magnitude) of each human-induced disturbance. Our aims were: (i) through the TAN approach, to carry out an arrangement and quantification of the main threats acting on our focal species and select the priority ones; (ii) through the TRA approach, to test the effectiveness of an operational project focused on mitigating the threats and improving the breeding success of species (i.e., building rafts and floating islands to encourage their nesting). Using the TAN approach, experts identified the following human-induced threats (IUCN code): 6.1—Generic disturbance; 7.2—Water stress; 7.3—Salinization; 8.8—Vagrant dogs; 8.8—Mediterranean gulls; 8.8—Wild boars, all significantly different in their magnitude. Among them, wild boars and Mediterranean gulls appeared the priority threats with the greatest extent, intensity and magnitude. Using the TRA approach, after the project, we assessed an overall decrease in the threat magnitude of 23.08% (21.42% when considering only the threats directly affected by our project). These data suggest that further efforts should be devoted to achieving greater effectiveness of conservation actions focused on our target species. With limited time and resources to quantify threats, expert-based approaches could be useful for rapidly assessing the effectiveness of small conservation projects by providing a range of scores obtained following an analytical procedure. In this regard, Threat Analysis and Threat Reduction Assessment could be considered useful tools to support adaptive management in project management cycles.