1)The species reproducing without a partner is more susceptible to infections and the like because its gene pool is not as diverse (sexual reproduction “shuffles” the genes producing new combinations and can even create new gene variants), therefore natural selection can't act as quickly as in the other species. Conversely, the parasites have an easier time adapting to the largely static genotype found in animals that reproduce asexually.

2)Because only very few fish manage to jump up the stream, the gene pool of the sexual species gets smaller and smaller as it moves up through the puddles. By the time the sexual fish have reached the upper pond, they are genetically very similar, losing their advantage over the species reproducing without a partner.

3)To restore the infection distribution seen in the lower pond, you could take a few fish from there and drop them in the uppermost pond, thus diversifying the gene pool of the sexually reproducing fish.