Bhutan, a small developing country, is recognised for its pro-environmental and unique development philosophy called Gross National Happiness (GNH). Over the years Bhutan has continually increased the area coverage under protected area (PA) system and probably it is the first country in the world that has achieved a 50% protection target. Going beyond the year 2020, there is a growing call to protect at the least 30% of the World’s terrestrial areas by 2030 with the ultimate goal to protect 50% by year 2050 - a goal commonly termed “Nature Needs Half’ (NNH). However, PAs globally and in Bhutan have been designated to protect terrestrial ecosystems and biodiversity. Although freshwater ecosystems and biodiversity are most threatened, there are very few freshwater specific protected areas while they are included within existing PAs by coincidence. The overall objective of this thesis is to assess the potential of existing terrestrialfocussed protected areas of Bhutan in conserving freshwater ecosystems and biodiversity within the context of nature needs half target and protected area dynamism. To achieve this, I have combined a systematic archival literature review with species distribution modelling and systematic conservation planning techniques to address four main issues: (1) the lack of a country level PA dynamism study and possible link between it and GNH, (2) lack of adequate freshwater species distribution data in Bhutan, (3) the need to assess potential of existing PA system for freshwater protection in the context of NNH, and (4) the need for systematic freshwater conservation planning in the context of NNH and PA dynamism. To address the first issue, I conducted systematic archival literature review on PA dynamism in Bhutan for almost the entire modern conservation history of Bhutan (1966- 2016). PA dynamism can be either of gain or loss events; the latter is termed protected area downgrading, downsizing and degazettement (PADDD). The conservation planning was the main proximate cause for PA degazettement and downsizing. On the other hand, an increase in infrastructure with hydropower development as the specific cause was the proximate cause for proposed PADDD. Overall PA dynamism reflected Bhutan’s commitment to environmental conservation guided by its GNH philosophy. I recorded differences in the number of PADDD events, PADDD types and PAs affected between the current study and those previously recorded for Bhutan from a regional level study. This demonstrated the need for country specific systematic archival literature search to better detect PADDD. To fill in freshwater species data gaps I curated georeferenced occurrence data of fish and odonata from the available literatures till 2017 and also through personal communications. While building SDMs for 10 fish and 28 odonates I compared the performance of four sequential model selection approaches against an expert (EXP) approach in selecting ecologically plausible species models. The sequential approaches using omission rate followed by test AUC (ORTEST) performed better over the sequential approaches that used omission rate followed by difference between training AUC and test AUC, and test AUC (AUCDIFF). ORTEST approaches could be used as a good first line model screening approach to reduce time taken by the EXP approach. This thesis contextualized freshwater biodiversity and ecosystems conservation against NNH by categorizing levels of species habitat, river length and lake surface area percentage protection into four progressive targets based on Aichi target 11 and NNH target. Despite covering 50% of Bhutan’s total land area, many freshwater ecosystems and taxa were inadequately represented within the existing PA system of Bhutan. These gaps could be easily filled employing Marxan, a common systematic conservation planning tool. Even when considering hydropower developments, we found solutions that increased the species coverage significantly. That said, high percentages of selected areas are already protected by the existing PA system. This suggests Bhutan may not need to change drastically the existing PA system if PAs are redesigned to better represent both freshwater species and forest types. This thesis provides the first real world example of inadequacy in protecting freshwater ecosystems and biodiversity by terrestrial-focused PAs even when total area of PA system meets the NNH target. The findings also demonstrate a clear need for freshwater conservation planning. The collated species occurrence data and ecologically plausible SDMs chosen here could be a starting point for freshwater conservation planning in Bhutan. The thesis also showed clear need to conduct country level systematic archival literature review to better detect PADDD. This thesis also linked PA dynamism study with freshwater systematic conservation planning and probably this could be way forward to design robust PA systems.