Abstract. We present spectroscopic monitoring of the Wolf-Rayet (WR) star WR 46 between 1989 and 1998, which has been obtained simultaneously with multicolour photometry (Veen et al. 2002a, Paper I). The spectroscopic monitoring data show that the radiative fluxes of the optical emission lines (O vi 3811/34, O vi 5290, N v 4944, N v 4604/20, He ii 4686, He ii 4859, He ii 5411, He ii 6560) vary in concert with the photometric single-wave (sw) frequency fsw (Paper I), and also the difference of that period between 1989 and 1991. The line-flux variability does not provide obvious support for a short second period (Paper I). The radial-velocity variations show a remarkable behaviour: usually, they display a coherent single-wave on the time scale of the double-wave period, while during some nights the radial velocity appears surprisingly to stay constant (see also Marchenko et al. 2000). These so-called stand-stills may be related to the observed time-delay effects. A time-delay effect manifests itself in several phenomena. Firstly, the line flux shows small, but persistent, time-delays for lines originating from lower optical depths, the outer-wind lines (N v 4604/20 and He ii). Secondly, the radial-velocity variations display much larger time-delays than the line fluxes and their behaviour appears less consistent. Assuming that the double-wave period controls the radial velocity, the stand-still is observed to start when the radial motion is in anti-phase with the presumed orbital motion. Thirdly, the outer-wind lines are observed to enter a stand-still much later than the inner-wind lines. Fourthly, the radial-velocity variations of the peaks of the emission lines precede the radial-velocity variations of the wings of those lines. In addition to line-flux-and radial-velocity variability, the He ii 4686 emission line shows pronounced line-profile changes on a time scale of hours. Our monitoring is not sufficient to study this in detail. Furthermore, we discern a flaring behaviour, i.e., an emission bump appeared on the blue wing of two He ii-lines (around −1700 km s −1 ) lasting less than 5 min. Finally, the line fluxes follow the observed brightenings, also on a time scale of years. We conclude that the short-term cyclic variability confirms the WR nature as established from the WR standard model analysis by Crowther et al. (1995; hereafter referred to as CSH). The various time-delay effects are consistent with the formation of the spectrum in a stratified stellar wind. The outer layers trail the inner ones. The variability is inconsistent with the formation of the spectrum in a stellar disc as proposed by Niemela et al. (1995) and Steiner & Diaz (1998). The long-term cyclic variability of the brightness and line fluxes is related to an increase of the mass-loss-rate, and, possibly, to the period changes. The interpretation of the nature of the variability is deferred to Veen et al. (2002b, Paper III).