Streams draining the Luquillo Mountains are steep and characterized by their many boulders and series of pools connected by small waterfalls, jumps, and riffles. The water is clear, as runoff is chemically diluted and suspended particles are mainly transported during flood events (see article Climate and Hydrology). Stream ecosystem dynamics is strongly influenced by physical factors, such as the rapid change in elevation from headwaters to coastal plains, the intensity and frequency of rainfall events, and the high temporal variability of stream discharge. The isolation of Puerto Rico from continental sources of freshwater species results in an aquatic fauna low in diversity.
The stream fauna is dominated by decapods (i.e., shrimps and crabs), fishes, and aquatic insects. Shrimp have complex life histories, all native species are amphidromous. Adult shrimp inhabit streams, but the larvae have to migrate downstream to the estuary or to the ocean to develop into juveniles. Juvenile then migrate back to the headwater streams to complete their life cycle. This life strategy makes them particularly vulnerable to disruptions in stream connectivity to the ocean, like dams and water intakes. Along the stream network, shrimps have particular longitudinal distributions, with Xiphocaris elongata and Atya lanipes typically abundant in headwater reaches and Macrobrachium spp. dominating lower elevation reaches, but able to move into high elevation reaches. Shrimp play a major role consuming all types of resources in streams. Xiphocaris are important consumers of detritus, in particular leaf litter. Atya are very versatile and can consume fine particles that they remove from the water column with their modified legs and also consume benthic resources that they scrape from the bottom. Macrobrachium are predators and consume other shrimp and aquatic insects. All of them are highly omnivorous and probably undergo ontogenic changes in their food preferences. Interestingly, studies using stable isotopes have found that algal resources are important in the diet of all species of shrimp.
Fish are more abundant in lowland reaches, where they can compete and prey upon shrimps. The presence of waterfalls in many streams within the Luquillo Mountains limits fish distribution. As a result, shrimps dominate headwater reaches above waterfalls and fishes and shrimps co-occur in areas downstream of waterfalls. Sicydium plumieri, Gobiidae, is the only species that can overcome waterfalls and inhabit headwater streams in the Luquillo Mountains. Most fish species are predators and consume both shrimp and aquatic insects, except for Sicydium that consumes algae.
Aquatic insects are diverse and abundant in all reaches around the Luquillo Mountains. In terms of abundance, mayflies of the family Leptophlebiidae are dominant. Leptophlebiids are abundant in areas where shrimp are also abundant, suggesting a degree of facilitation between the two groups. Shrimp remove sediment from the stream bottom and mayflies benefit from particle free habitats that they use to graze algae. Most other insects appears to be negatively affected by shrimp and fish consumption. Studies assessing the abundance and composition of insect assemblages among different stream habitats show that insects are more abundant in those habitats where shrimps are absent (e.g., waterfalls, areas bedrock with a shallow sheet of water flowing over them).
Stream ecosystems within the Luquillo Mountains are vulnerable to hydrologic alterations from outside their boundaries. A water budget developed in 1994 indicates that on an average day more than 50% of stream water draining the Luquillo Mountains is diverted into municipal water supplies. While the forest has some of the last undeveloped water supplies on the island, water withdrawals conflict with other functions that the Forest fulfills, such as maintenance of biodiversity.
Some of the ecological research conducted within the Luquillo LTER has important applied value for stream management within and outside the Forest. The LTER has valuable information on: 1) long-term recording of migratory shrimp and fish populations; 2) in-stream flow habitat requirements of shrimps and fishes; 3) assessment of nocturnal behavior of shrimps and timing of larval shrimp migration to estuaries; 4) upstream migration of shrimps, fish, and snails; 5) effects of low-head dams and water withdrawals on shrimp and fish mortality; 6) effects of large dams on stream ecosystem characteristics; 7) genetics of shrimp populations; 8) impacts of water extraction and sewage release on water quality; and (9) effects of whole stream poisonings on shrimps and fish populations. More recently the LTER has focused on the effects of predicted increases in drought frequency due to global climate change.
Management recommendations from ecological research are being used to mitigate negative environmental effects of stream water withdrawals. For example, the designs of two new water withdrawal systems have been altered by the Puerto Rican Aqueduct and Sewage Authority to minimize mortality of migrating shrimps and fishes. Water intakes also operate when stream flows are high so that base flows are maintained. Equally encouraging is that water withdrawal from some intakes has been prohibited during peak larval shrimp migration (7 to 11 pm) and fish/shrimp ladders are now required. Stream research at Luquillo highlights the critical need to address cumulative long-term effects of hydrologic alterations on public lands and illustrates the synergism that can occur between field managers and scientists in implementing ecosystem management solutions.