The Amphora contains many marine as well as some brackishwater species, in spite of being considered as freshwater species (euryhaline), and species such as A. crassa, A. ovalis and A. ccoffeaeformis have excellent adaptability at relatively lower salinities in neritic sections of the coastal ecosystems so it was no wonder that it flourished in a slightly saline lake. May be there were no other equally or more adabtable competing species for the available resources at that time. Additionally my assumption is that due their greater surface area to volume ratio and ventral raphe systems they were more buoyant (slower sinking rates) in an environment with low water movement than many other pennate diatoms, hence enabling it to make the most of the resources. As you did not specify the algal composition of the lake my answer is also limited. I sincerely wish I was of more help.
Many species in Amphora sensu lato are marine but an increasing number of species are being described from inland habitats. However, in spite of recent revisions of Amphora s.l. that included the elevation to the generic status of the subgenus Halamphora (Levkov 2009), the genera Amphora and Halamphora still appear to be insufficiently known in freshwater habitats.
The salinity barrier dividing the freshwater from the marine realm was supposed to be virtually impassable but Alverson et al. (2007)
Article Bridging the Rubicon: Phylogenetic analysis reveals repeated...
showed that this did not apply to the thalassiosiroid diatoms.
More recently, Ruck et al. (2016),
Article Phylogeny, ecology, morphological evolution, and reclassific...
working on the Surirellales and Rhopalodiales, proposed an interesting ‘stepping-stone’ hypothesis, based on comparative molecular-phylogeny evidence supporting the idea that the ancestrally-marine diatoms belonging to these groups would have used brackish waters as an intermediate habitat to which to adapt before invading freshwater environments. In the light of these papers, the most recent study by Stepanek & Kociolek (2019)
Article Molecular phylogeny of the diatom genera Amphora and Halamph...
suggests that inland saline habitats are of particular interest for such studies: for diatom groups, such as Amphora and Halamphora, that have representatives
colonizing smaller inland waterbodies with elevated conductivity, these waterbodies might represent potential intermediate habitats from which the colonization of surrounding freshwaters could have taken place.
It thus makes sense from an evolutionary point of view that an Amphora s.l. species can become dominant in a slightly saline lake. However, as suggested by my Colleagues in previous replays, much more information on the taxon involved and on the environmental conditions would be needed to provide more ecological interpretation of your observation.