Biomonitoring, in its most liberal definition, is as old as humanity. Early humans would have been keenly aware of changes in animal and plant communities, especially those that were part of their prey and food supply, and they may have been able to make some tenuous connections between these changes and their changing environment. However, these early humans (and indeed many modern ones) would have been completely unaware of the changing populations of microscopic organisms under their feet, and what can be learned by scientific study of these sentinels.

The meiofauna is abundant and diverse, occupying key roles in sediment food webs and nutrient cycling, and responds rapidly to environmental changes. Nematodes and copepods usually constitute the major components of the meiofauna. As well as being a large part of the meiofauna, nematodes are the most abundant and most diverse invertebrates in many sediments and soils. They occupy a wide variety of ecological roles in sediments, and their community structure provides important clues to the structure of benthic foodwebs, as well as to responses of sediment ecosystems to environmental changes such as pollution and changes in tidal range. Despite the advantages of using nematodes for biomonitoring, they are used less frequently than other groups due to some major limitations, including the so-called "taxonomic impediment". Some aspects of this impediment are illustrated via the description of new free-living nematode species. One limitation is the scarcity of expert marine nematode taxonomists and the concentration of these experts mainly in Europe. The present study is the first to investigate Californian coastal nematodes to address environmental concerns in California, specifically the restoration-in-progress of the Bolsa Chica wetland. In common practice, nematode studies usually refrain from analyzing species-level differences between sites and communities, settling instead for genus or family level identifications by way of more feasible compromise. This choice is made perforce by the challenges of working with nematodes, and meiofauna in general. Part of the present study examined whether this choice is justified in the case of free-living marine nematodes. New molecular methods present opportunities to improve biomonitoring. Whole DNA extracts from a sediment core can be subjected to massively parallel pyrosequencing of taxonomically distinctive DNA loci, producing in one procedure a comprehensive list of the great majority of interstitial invertebrates living in that sediment across most animal phyla. Determining how the detailed and relatively robust phylogenies created with these new molecular tools can be incorporated in the study of biodiversity is an important research area, as biodiversity is the main facet of biomonitoring.

Flows in tidal marshes arc not described well by the classical equations of open channel flow. The geometry of the marsh complicates analysis of the system. Water depths in tidal marshes are usually small, varying from a few centimeters or even dry at low tide to a meter or more at high tide. At low tides, the flow can be channelized and is often essentially one-dimensional. At high tides the system frequently must be described using a more complete two-dimensional approximation. A model is thus required that permits transitions between differing areas of the system. It must accurately represent the changes of the areas inundated during the tidal cycle. It must also be capable of operating to the resolution necessary to characterize the flow regime in the marsh.

Vegetation within the marsh presents a variable resistance to flow particularly in this range of depths. A parameter like Manning's n is insufficient to characterize the variable friction resistance to flow. A new formulation is required which accounts for head losses within the vegetation as well as flow transitions between the channels and vegetated marsh surface. This formulation will be independent of the model used and is relevant whether the model is one-dimensional or two-dimensional. Factors that contribute to head losses in marshes are: turbulent energy losses, bottom friction, wind stress, drag from the erect plants that obstruct the flow, and secondary currents within the vegetation. The relative magnitudes of these effects have not been quantified impervious research. Direct observation of small scale hydrodynamic phenomena is difficult because of the shallow depths, frequently inaccessible field conditions during high tides and the spatial heterogeneity over the marsh surface. Most computation of flow in tidal marshes is carried out using the lumped friction parameter of classical open channel flow. This parameter is a calibration coefficient and has only a limited physical basis.

An additional problem that must be addressed is the influence of tidal marsh inundation on the circulation within the estuary proper. Typical estuary models build the equivalent of sea wall on the estuary perimeter. Depths at these locations typically do not go to zero and the marsh behind these arbitrary boundaries is excluded from the analysis. A model is thus required that can cost effectively and accurately incorporate these areas into the estuarial analysis.

An ecological model incorporating benthic algae was developed using an existing unsteady one and two-dimensional water quality model (RMA-4q) to transport constituents in the water column. The types of benthic algae simulated are attached filamentous algae (e.g. Cladophora) and perilithic biofilm. These are influenced by different physical processes, although hydrodynamic detachment occurs with each. Attached filamentous algae occur in the turbulent flow region and access to nutrients is assumed not to be limited by diffusion, as is the case for perilithic biofilms. The biofilrn equation solution is therefore more difficult to solve. The theoretical development of the equations for each benthic algal type is presented, along with numerical solution schemes. Field data collection methods and their results are discussed. The data are used in support of the modeling effort. Finally, results from an example application for the Russian River are given. The effect of nutrient loading and hydrodynamic detachment are evident. Problems with temperature and its relation to system geometry are discussed. Topics for future research are presented.