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Ferns boast an independent gametophyte generation that apparently lacks effective means of regulating water loss. Specific mechanisms of fern gametophyte survival in dry regions remain unknown. We seek to understand fern adaptation to seasonal drought by examining gametophyte response to desiccation in situ. During seasonal desiccation, we measured microclimate drivers (humidity and temperature) and physiological response (thallus area and dark-adapted chlorophyll fluorescence). We found that the microclimate typically varied between fern sporophyte leaves and gametophyte thalli, but not between fern and moss gametophytes. Fern and moss gametophytes remained physiologically active for ~2 months after the last rain event, with gradually decreasing thallus area and chlorophyll fluorescence until thallus area reached <20% of pre-desiccation values and fluorescence reached zero. All fern and moss gametophytes recovered completely following rehydration, reaching the same pre-desiccation area and fluorescence after irrigation and the natural rain event. Our study is the first to report desiccation tolerance in chaparral fern gametophytes. The humid microclimate at the soil surface apparently prolongs seasonal dehydration and improves desiccation tolerance compared to rapid drying trials. These findings provide insight into the specific conditions required for successful desiccation tolerance in fern gametophytes and the survival mechanisms of this seemingly delicate stage in the fern life cycle.