**Gonzalo C. Castillo**

Lodi Fish and Wildlife Office, U.S. Fish and Wildlife Service, Suite 105, 850 S. Guild Avenue, Lodi, CA 95240, USA; gonzalo\_castillo@fws.gov; Tel.: +1-209-334-2968 (ext. 418)

Received: 26 March 2019; Accepted: 24 May 2019; Published: 3 June 2019

**Abstract:** The aim of this community modeling study was to evaluate potential mechanisms by which freshwater outflow in the upper San Francisco Estuary, CA, controls the fall habitat and abundance of subadult delta smelt *Hypomesus transpacificus* and its community. Through analyses of the community matrix, community stability and the direction of change of community variables were qualitatively and quantitatively modeled under four outflow–input scenarios. Three subsystems were modeled in the low salinity zone (1–6 psu), each overlapping the location corresponding to the distance from the mouth of the estuary to upstream positions where the near-bottom 2 psu isohaline (X2) is at 74, 81, and 85 km (corresponding to high-, mid-, and low-outflows). Results suggested communities were qualitatively stable at each X2 position, but simulations showed the percent of stable models decreased from low- to high-X2 positions. Under all outflow–input scenarios, the predicted qualitative population responses of delta smelt were: (1) consistently positive for the low X2 position, and (2) uncertain under both mid- and high-X2 positions. Qualitative predictions were generally consistent with quantitative simulations and with the relations between relative abundance of delta smelt and X2. Thus, high outflow seems beneficial to subadult delta smelt when X2 reaches 74 km during fall.

**Keywords:** biological communities; transitional waters; community matrix; qualitative model; species interactions; freshwater flow; low salinity zone; simulation; ecological assessment; adaptive managemen<sup>t</sup>
