Consider the following list of non-native prefixes, taken from Booij (1995):

Non-native prefixes never carry primary word stress. Yet they can carry secondary stress if there is at least one intervening syllable between the first syllable of the prefix and the primary stress of the word. In that way, non-native prefixes behave like monomorphemic words; such words have have a predictable initial secondary stress – with the exception of cases in which the second syllable carries primary stress, as adjacent stresses within a prosodic word are disallowed and always have to be split by at least one unstressed syllable.

This predicts that monosyllabic prefixes should receive secondary stress if their base word does not have initial stress, while polysyllabic prefixes with a stressable first syllable should always receive initially stress on that syllable.

This is indeed the case. Consider first the prefix re-. For instance, in the word reductie [re.ˈdʏk.si] reduction, the prefix is followed by the main-stressed syllable of the word. Accordingly, the prefix remains unstressed and the vowel in the prefix re- can optionally be reduced to schwa ( [rə.ˈdʏk.si]), which is an indication that the main stress directly follows the prefix. Reduction, however, is impossible in representeer [(ˌ)re.pre.zɛn.ˈter] (I) represent, as the main stress is not adjacent to the prefix: secondary stress can be assigned to the initial syllable (since this would not result in a stress clash), and the syllable is not reducible. As the phonological makeup of these prefixed forms usually resembles that of monomorphemic words, and as their meaning is not transparent, it is often questionable whether they still classify as prefixes, or whether they rather form one unit with their base word.

The main distinction between non-native and nativized prefixes lies in their combinability with native base words. While non-native prefixes never combine with native base words, nativized prefixes can do so; some of them can even occur as independent words, as for instance anti-, co-, contra-, des-, ex-, inter-, meta-, non-, para-, pro-, semi-, sub-, super-, ultra- (see Booij 1995:120). Notably, these prefixes always receive primary stress when combined with nouns, and they never syllabify together with a noun; this indicates that, unlike non-native prefixes, they are independent prosodic words and form compounds with their base words. Consider the following examples:

Note that in adjectival compounds, nativized prefixes do not attract primary compound stress – in such cases, primary compound stress falls on the adjective (in predicative position, while it shifts leftwards in attributive position; see Langeweg 1988):

Largely based on Booij (1995), we divide native prefixes into three main classes with respect to their stress behavior. Some native prefixes attract main stress when they combine with a noun; such prefixes therefore behave like independent prosodic words, as they receive primary compound stress (at least when combined with nouns, which display the large majority of relevant words). On the other hand, there are native prefixes that never carry stress; these prefixes create verbs, and they also occur as particles or prepositions. There is also a small group of prefixes that, when used with base verbs, are situated in between the stress-attracting and the stress-avoiding ones; they sometimes attract stress: we refer to this group as intermediate.

These prefixes usually combine with nouns and attract main stress (Booij 1995). As a result of this, they behave like noun compounds and receive initial compound stress. Consider the following overview (taken from Booij 1995:121):

Dutch has two types of (verbalizing) prefixes that never attract stress. The first one consists of prefixes whose only vowel is a schwa; as schwa never carries stress, these prefixes accordingly never carry stress either (overview from Booij 1995:122):

The second group of stressless native prefixes contains prefixes that independently occur as prepositions. They all contain a full vowel: consequently, they meet the requirements of forming prosodic words on their own. As they do not receive primary compound stress, we can conclude that they do not behave like most nominal compounds (which show a strong-weak pattern). Their stress pattern rather resembles the weak-strong pattern found in a variety of adjectival compounds. However, while adjective compounds often show stress shifts in attributive position, such stress shifts do not occur for the prefixed verbal forms. The overview is taken from Booij (1995:122):

When combined with verbal bases, the prefixes her-, over- and onder- sometimes carry stress and sometimes they do not: they attract stress if the first syllable of the following base verb does not carry main stress but in cases in which the base verb shows initial stress, stress is realized on the base verb (Schultink 1964, De Vries 1975). Consider the following examples:

Prefix	Base verb	Derived verb
her-	halen [ˈha.lə(n)] fetch, get	(ik) herhaal [hɛr.ˈhal] (I) repeat
	formuleren [fɔr.my.ˈle.rə(n)] formulate	(ik) herformuleer [ˈhɛr.fɔr.my.leer] (I) reformulate, (I) rephrase
over-	komen [ˈko.mə(n)] come	overkoom [o.vər.ˈkom]
	belichten [bə.ˈlɪx.tə(n)] lighten	(ik) overbelicht [ˈo.vər.bə.lɪxt] (I) overexpose
onder-	schatten [ˈsxɑ.tə(n)] estimate	(ik) onderschat [ˈɔn.dər.sxɑt] (I) underestimate
	betalen [bə.ˈta.lə(n)] pay	(ik) onderbetaal [ˈɔn.dər.bə.tal] (I) underpay

In the literature it has been pointed out that the behavior of the prefix on- is marked (Van den Berg 1970, Schultink 1979, Booij 1995): when combined with adjectives, on- is usually unstressed in predicative position (stress is realized on the stem) but regularly receives stress in attributive position:

Alternatively, in predicative position, stress can be realized on on- “to emphasize the negative meaning”(Booij 1995:123). According to Booij, this is not possible in adjectives where on- is semantically opaque.

The same applies to the prefixes aarts- and oer-(Booij 1995:123).

Note that these forms display the same stress patterns like most adjectival compounds with respect to the stress alternation between predicative and attributive position (as opposed to nominal compounds which do not show stress shifts).