The systematics of Alburnoides taxa from the western Balkan region remains unresolved, and they are sometimes described as belonging to the "Alburnoides prespensis complex".

In particular, the results of molecular analyses suggest that the congeners A. devolli and A. fangfangae, plus subpopulations inhabiting the Vjosa (el. Aoös), Skhumbin, Dukati and Borsh river systems in Albania and Greece, might be conspecific with A. prespensis (Geiger et al. 2014, Jouladeh-Roudbar et al. 2016, Stierandová et al. 2016, Tsoupas et al. 2022).

Global and European regional assessment: Endangered (EN)
EU 27 regional assessment: Endangered (EN)

The Prespa Spirlin has a restricted range (extent of occurrence (EOO) c. 1,592 km²), which meets the threshold for the Endangered category under Criterion B1 (EOO < 5,000 km²). It is present at two locations where the extent and quality of habitat are estimated to be declining. Therefore, this species is assessed as Endangered under Criterion B (B1ab(iii)), both globally and for the EU 27 Member States.

This species is endemic to the Lake Prespa (sq. Liqeni i Prespës; mk. Преспанско Езеро; el. λίμνη Πρέσπα) transboundary basin, which is shared by Albania, the Republic of North Macedonia and Greece.

This species' current population size and trend have not been quantified. Field observations indicate that its population size has reduced since the 1980s.

The Prespa Lakes basin lies at 850 metres AMSL and is a hotspot for endemic biodiversity, including freshwater fishes and migratory birds. It comprises two relatively shallow interlinked lakes; the larger Greater Prespa (el. Μεγάλη Πρέσπα; mk. Преспанско Езеро; sq. Liqeni i Prespës së Madhe) and Lesser Prespa (el. Μικρή Πρέσπα; mk. Мало Преспанско Езеро; sq. Prespa e Vogël), which are separated by a narrow strip of alluvial land.

The catchment is fed solely by precipitation and snowmelt. It partially drains to nearby Lake Ohrid (sq. Liqeni i Ohrit; mk. Охридско Езеро), and by extension the Drin (sq. Drini; mk. Дрим) River system, via subsurface karstic conduits.

The Prespa Spirlin is most commonly found in littoral zones of the lakes, plus stretches of affluent streams and rivers with clean, flowing, well-oxygenated water.

Spawning reportedly takes place over sandy or stony substrata during late spring and early summer.

The Prespa Lakes have been partially modified. They are connected by a man-made channel excavated through the alluvial isthmus which separates them, on which a controllable sluice is installed, and was reconstructed in 2004. In addition, a minor natural outflow from the Agios Germanos River delta to Lesser Prespa was blocked during the 1930s and has not been restored, reducing the volume of water that flows into the lake.

In Albania, Lesser Prespa was for a number of years artificially connected to the Devoll River via the so-called Prespa Canal Scheme in order to abstract water for irrigation purposes, but the project was abandoned and the canal filled in during the early 2000s after it failed to function as planned. During the period that the canal was open, sedimentation in the southern portion of Lesser Prespa increased drastically, leading to a pronounced reduction in water depth and expansion of reedbeds in littoral zones.

Ongoing water abstraction for agricultural and domestic use takes place throughout the basin. Water abstraction has been cited as the central cause for the continued diminishing water level in Greater Prespa, which has receded by at least eight metres since the mid-20^th century. Climate change is a secondary driver of the falling water level, with a significant decrease in discharge, winter precipitation and snowfall observed since the 1960s. The situation is so drastic that the sluice gate between the lakes has to be kept closed at all times in order to maintain the water level in Lesser Prespa, which is now located at a higher altitude than Greater Prespa and would otherwise drain into it.

The reduction in water volume, coupled with an increase in nutrients, toxic substances and solid materials (including plastics) entering the lakes from surrounding farmland, industry (small-scale food processing, poultry farming, textiles, metal processing, wood processing, civil construction, ceramics and chemicals), illegal landfills, fly-tipping and untreated domestic wastewater has resulted in escalating eutrophication. This is particularly evident in Lesser Prespa, where blooms of toxic cyanobacteria now occur on a regular basis during summer and autumn. Construction of small dams on streams draining into Greater Prespa has blocked access to some spawning grounds used by native fishes, with additional projects planned.

At least 13 non-native freshwater fish species have been introduced to the Prespa basin, of which at least six have become established. These include the Topmouth Gudgeon (Pseudorasbora parva), Pumpkinseed (Lepomis gibbosus), Common Carp (Cyprinus domestic strain) and European Bitterling (Rhodeus amarus), all of which are considered invasive and can exert detrimental pressures on native freshwater fauna through increased competition, predation, habitat degradation or transmission of pathogens.

The Prespa Lakes support a commercial fishery, but this species is not targeted.

This species is included in Appendix III of the Bern Convention (as Alburnoides bipunctatus).

No specific conservation management plan exists, but a number of protected areas lie within the boundaries of its range. The entire Prespa Lakes basin falls within the limits of the Prespa Park, the first transboundary protected area in the Balkan Peninsula. The Prespa Park was established in 2000 in response to environmental concerns regarding the lakes, following a joint trilateral declaration by all three bordering countries, but was not formalised until 2017. The lakes are also surrounded by four National Parks, and two sites within the basin are included in the European Union's Natura 2000 network of protected areas. In addition, both lakes are designated as Wetlands of International Importance by the Ramsar Convention on Wetlands.

Since 2005, the Prespa Park Management Body controls the volume of water exiting Lesser Prespa to Greater Prespa by regulating the outflow discharge on the artificial channel connecting the two lakes. The environmental organisation 'Society for the Protection of Prespa' currently coordinates a transboundary environmental monitoring system within the Prespa basin, which includes tri-annual fish surveys. The European Union co-funded LIFE project 'Prespa Waterbirds' (LIFE15 NAT/GR/000936) ran from 2016-2021 and aimed to contribute to waterbird conservation in Lesser Prespa via a series of actions, including a specific plan to improve "spawning grounds and access for fish species". Specific actions included the clearing of sediment and reedbeds from around the mouths of tributary streams to facilitate the passage of migratory fishes.

An earlier LIFE project (LIFE2002 NAT/GR/8494) also targeting bird conservation took place from 2002-2007 and aimed to "increase fish spawning grounds", while the Global Environment Facility project 'Integrated Ecosystem Management in the Prespa Basin in Albania, FYROM and Greece' ran from 2006-2011. Furthermore, a LIFE+ Information and Communication Project entitled 'Fish, Fisheries & European Policy' in the Prespa Basin (LIFE09 INF/GR/000319) was funded from 2010-2013 with the objective to "promote the conservation of the threatened endemic and rare fish fauna of the area and the implementation of sustainable fishery practices".

The introduction of non-native species to the Prespa Lakes has been outlawed, and strict annual catch limits are in place for the native fishes of commercial interest. Fishing of any kind is also forbidden during mid-to-late spring, when native fish species spawn. Fly-tipping, disposal or processing of any kind of waste, discharge of untreated waste water, shoreline construction, excavation of sand or gravel, unlicensed use of lake water, uncontrolled cutting of trees and forests, and inappropriate utilisation and burning of pastures have all been prohibited.

This species' population status, life history, habitat preferences, and response to the ongoing threats in the Prespa basin are poorly understood, and further research is required.

It is recommended that future research should focus on resolving the Prespa Spirlin's taxonomy (see 'Taxonomic Notes') prior to understanding its population status, life history and response to the identified threats.