That’s an important issue. As you probably know, some fish species travel upstream to reproduce. If they can’t get over the dam, that species is probably doomed to extinction. One solution is “fish ladders,” which are sort of like stairs for fish. These are usually off to the side of a dam and have water flowing over steps that the fish can climb. Some research shows that fish ladders are not very effective. One study showed that only 3% of fish made it to their spawning grounds. Some high mountain lakes are artificially stocked be dropping hatchery-raised fish out of helicopters.

One solution is to actually remove dams. There is a growing trend to get rid of dams that are not necessary. Some dams were created to provide recreation. Others were used for power in the past, but are no longer used or needed. Some were built for flood control. Unfortunately, while dams are helpful in preventing frequent, small floods, they can actually cause massive floods if the dams fail or the reservoirs get too full. Removing dams can improve water quality, habitat, and other forms of recreation. Dam removals are not popular with people who had a house near a lake and now have a house near a large mud puddle. The mud will probably grow over into a meadow, and then a forest over the coming years. But that may not make the homeowners happy if they prefer a lake.

If you’re interested in issues like this, you may want to study conservation biology.

Producing energy usually involves tradeoffs, and it’s often unclear what the best solution is. Hydroelectric power sources, including dams, have been described as more environmentally friendly than fossil fuels because they produce smaller amounts of pollutants. However, recent research suggests that dams produce significantly more greenhouse gases due to decaying vegetation than was previously thought. Furthermore, as you point out, dams change local ecosystems and threaten local wildlife. Dams trap sediment, changing the environment both upstream and downstream of the dam, and prevent fish from migrating.

Three ways in which the threat to wildlife can be reduced are engineering systems of dams, design changes to individual dams, and changing operation procedures of dams. For a system of dams on a river, some researchers have suggested that slight reductions in the total number of dams may greatly reduce the harm to fish populations while maintaining most of the energy output. Individual dams can be engineered to include bypass channels to allow fish and sediment to pass through. Other methods of moving fish across a dam include fish ladders, elevators, and cannons. Changes to dam operation include fully opening dams in certain seasons to help restore the native ecosystem, gradually changing the flow of water through a dam rather than abruptly changing flow in response to energy needs, and the area upstream of dams can be sluiced and flushed to move sediment downstream.

To effectively protect ecosystems, new dams should be built and operated with these changes, and old dams should be upgraded. This is a political issue, as improvements to dams generally require tax dollars. Ultimately, the environmental impact of dams will be determined by how much people are willing to pay to protect their environment.

With difficulty, it appears. From the information that I found all seems to be related to the danger, not the protection. Here are the first 2 hits I got: dams-fish-fisheries

"The construction of a dam on a river can block or delay upstream fish migration and thus contribute to the decline and even the extinction of species that depend on longitudinal movements along the stream continuum during certain phases of their life cycle."

Implications of Dam Obstruction for Global Freshwater Fish Diversity: read here

The article above is by CR Liermann - ‎2012 - ‎Cited by 186 - ‎Related articles Jun 1, 2012 - A synthesis of obstruction data and fish traits indicates that taxa such as lampreys (Lampetra spp.), eels (Anguilla spp.), and shads (Alosa spp.) are at particular risk of species loss. Threatened eco-regions with heavy dam obstruction and above-average counts of total, diadromous, or endemic species are found on all continents.

Well, one simple way is simply to remove the dams. Unfortunately that causes a host of other problems that are not so simple. One way would be to move the species around with human help, but that only works for species that we humans know exist and that we can move. In practice, it isn't easy.