Polyynes, linear sp-carbon chains of finite length, can be synthesised by submerged arc discharge in liquid, which so far, has been mainly exploited in organic solvents.In this work, we investigated the technique in water as a cheap and non-toxic solvent to produce polyynes. After optimisation of the process parameters, hydrogen-terminated polyynes (CnH2: n=6-16) were identified by high-performance liquid chromatography with the support of theoretical calculations. Size-selected polyynes were separately analysed by surface-enhanced Raman spectroscopy allowing to assign the bands of mixed polyynes solution to specific wire lengths. Stabilisation strategies for hydrogen-capped polyynes were also studied, obtaining promising results.