A warmer climate accompanied by changes in precipitation patterns will affect hydrologic regimes, biogeochemical cycling, community composition and productivity, and wetland ecosystem structure and function (Arnell and Gosling 2013, Grimm et al. 2013, Pyne and Poff 2016, van Dijk et al. 2015). Sea level rise will likely inundate many areas, increasing the salinity of freshwater wetlands, triggering salt water intrusion in aquifers and altering biotic communities and water quality (Craft et al. 2009; Weston et al. 2006). Alterations to natural disturbance regimes, such as fire or intense hurricanes, could also have significant effects on freshwater health (Michener et al. 1997). Shifts in the frequency, timing and intensity of rainfall events can affect the transport of sediments, nutrients and other constituents from wetlands as well as precipitate larger flooding events (Arnell and Gosling 2016). Perturbations in hydroperiod and hydrologic flows can significantly affect aquatic communities and associated biogeochemical processes that ultimately have effects on water quality (Delpla et al. 2009). The temporal sensitivity of freshwater resources to climate change ranges from within-year to annual to multi-year to centuries (Ford and Thornton 2012).

The Ecosystem Vitality and Ecosystem Services components will be the most relevant for examining the effects of climate change on the indicators. Evaluation of the indicators under climate change scenarios should use the underlying hydrologic model as the foundation to which climate-related data is linked. Projected changes in precipitation will be of most relevance in assessing the effects of climate change on hydrological systems, and this will directly affect evaluations of deviation from natural flow regime and change in groundwater storage. Ideally, projections of precipitation should be based on established general circulation models most suitable for the basin; they should span a range of low to high emissions scenarios; and they should be downscaled to a meaningful or readily available spatial scale. In the absence of such data, hypothetical scenarios can be used to explore the effects of changes in precipitation, e.g., baseline scenario plus or minus 10% change in rainfall. The outputs of the hydrologic model with projected precipitation then feed into other models in the model chain (Figure 3) to enable calculation of other indicators (e.g., water quality, flood damage models).

Changes in temperature may also affect the biotic components of freshwater ecosystems, such as the population sizes of species of concern and invasive species. This will be difficult to estimate and will rely on information on physiological tolerances. However, changes in the distribution of species habitat due to changes in precipitation and temperature can be modeled using Species Distribution Models (SDMs), which indicate relative changes in biodiversity.

To fully evaluate effects of sea level rise on coastal basins, a fully three-dimensional (3-D) circulation model of the basin, such as that described by Zheng and Weisberg (2012), is recommended (NRC 2014). Ideally, this should be coupled with a regional hydrologic model and a regional atmospheric model (e.g., Maxwell et al. 2011). Understanding salinity intrusion in coastal wetlands and aquifers used for water supply requires a surface water flow model coupled with a variable-density groundwater flow model. Since it is unlikely that this is possible for most coastal basins, it will be necessary to include the effects of sea level rise in a piecemeal and incomplete fashion without the benefit of a systems model that couples all the relevant components. To this end, plausible hypothetical scenarios (e.g., 1.5-meter sea level rise) may be the only option in examining the effects of sea level rise on freshwater systems. In such cases, it will also be necessary to consider the range of effects this has on the indicators most likely to be affected. For instance, underwater quality, it will be necessary to consider a measure of salinity in the climate change scenario analysis even if that was not considered in the baseline assessment.

It is noted that three major areas of uncertainty are at play in decision making in the face of climate change: 1) uncertainty in the climate projections due to the different general circulation models (GCMs) employed and the gas emission scenarios used as input for these models (IPCC 2014), 2) uncertainty in the impacts to freshwater ecosystems and hydrology under these projections, and 3) uncertainty in the effects of specific management and planning decisions on freshwater systems under climate and associated changes (Lawler et al. 2010).